The government is still intensively monitoring Lincoln University's finances, but is encouraged by its progress, Tertiary Education Minister Steven Joyce says.

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The university has suffered a string of deficits and falling student numbers, and a $100 million government investment in a planned research hub with Crown research institutes is running about a year late.

But Mr Joyce said the university had reported increasing enrolments by new students and he expected to receive the business case that would unlock funding for the research hub very soon.

"Lincoln is still on intensive monitoring in relation to their financials and that's appropriate, because as you've noted their annual report indicates that they've made a loss before earthquake impacts of about $5 million," he said.

"So yep, we're intensively involved and it's a challenging environment - they're a small specalist university - but they're making the right steps and I'm encouraged by what they're doing."

A key part of Lincoln's plans is a research and teaching hub for the land-based industries in conjunction with three Crown research institutes and DairyNZ.

The government agreed in principle in mid-2014 to provide $107m toward rebuilding Lincoln's earthquake-damaged science facilities as part of the hub project, but the money has still not been provided.

Mr Joyce confirmed the delay was because the government had not been satisfied with the university's original plans.

"We were concerned initially that their projections weren't realistic enough and they've taken that on board and they're rearranged both their projections of numbers of students and also therefore their expectations of what facilities they need."

Lincoln's vice-chancellor, Robin Pollard, started work at the university three months ago.

He said the university was undergoing rapid change including to its management structure.

"I've put in place a number of change proposals, made a number of changes, so things are moving along pretty quickly."

Dr Pollard said the university had agreed with five shareholders to form a Lincoln hub company and he expected the government would make an announcement about that project in July.

He said student numbers were not a good measure of universities' viability because different students provided different amounts of income, but he confirmed that Lincoln intended to increase its enrolments.

"We are looking in the ten-year plan for another 1200, maybe 1300 students. A large proportion of those, maybe 50 percent, will be research students, masters and PhD level, and the rest will largely be international. But there is more to a university's viability than student numbers."

Dr Pollard said the university was expecting to make a deficit this year.

However, commencing-student numbers increased this year and last year and he was confident the university would get back on its feet.

Lincoln's 2015 annual report showed that it made a surplus last year only because of a $27 million insurance payout for earthquake damage.

It said the university had 2934 equivalent full-time students last year, 50 fewer than in 2014.

University annual reports

All eight universities reported surpluses for 2015.

The Tertiary Education Commission recommends tertiary institutions make surpluses equivalent to between 3 to 5 percent of their income and only the University of Canterbury and Massey University were below that level.

Canterbury's surplus was 1 percent and Massey's 1.3 percent.

Canterbury had 11,931 equivalent full-time students, 12 fewer than in 2014 and well below a high of 15,494 in 2010 - the year before the university's buildings and enrolments were hurt by the Canterbury earthquake.

Massey University had the equivalent of 18,688 full-time students, just eight more than in 2014, and 6000 of them were enrolled in its distance education programmes.

The largest university, the University of Auckland, recorded a surplus of 6.3 percent, $67.4 million.